Weber State University       Department of Botany

BTNY LS1203 - Plant  Biology

Basic Chemistry

element = a substance that cannot be broken down into a simpler substance by ordinary chemical means

Periodic Table of the Elements

atom = the smallest possible amount of an element (Fig 2.1)
        protons: charge = +1, weight = 1 atomic mass unit or dalton
        neutrons: charge = 0, weight = 1 dalton
        electrons: charge = -1, weight ≈ 0 dalton
        protons + neutrons form the nucleus of an atom
electrons orbit the nucleus, with each electron located at a specific energy level or electron shell

atomic number = # protons
atomic mass = neutrons + protons

H = hydrogen. 1 p+, 1 e-
C = carbon. 6 p+, 6 n, 6 e-

Isotopes: same number of protons, different number of neutrons. (Fig. 2.3)
There are three isotopes of H:
¹H (1 p+), ²H (1 p+, 1 n), ³H (1 p+, 2 n)
There are also three isotopes of C:
¹²C (6 p+, 6 n), ¹³C (6 p+, 7 n), ¹⁴C (6 p+, 8n)

Na = sodium. 11 p+, 12 n, 11 e-
Cl = chlorine. 17 p+, 18 n, 17 e-

Ions and Ionic Bonds (Fig 2.7)
Ion = charged atom or molecule (Na⁺, Cl-, Mg²⁺, NH₄⁺, NO₃^- )  Ionic bonds form by attraction of oppositely charged ions. The crystals that form are generally referred to as salts. Ionic bonds are easily broken by dissolving the salts in water.

Covalent Bonds  (Fig 2.6)
Form by the sharing of electrons. Atoms that share a single pair of electrons are linked by a single bond. Atoms that share two pairs of electrons are linked by a double bond. Atoms that share three pairs of electrons are linked by a triple bond. Atoms that are linked by covalent bonds form molecules: O₂, H₂O, CH₄

Carbon can form 4 covalent bonds. In biological molecules, the bonds are primarily to H, oxygen (O), nitrogen (N), and sulfur (S). Many biological molecules contain phosphorus (P), but it is always present as phosphate (PO₄^3-), with C bonded to one of the O atoms in phosphate. (Fig 2-12, Fig 2-15)

Polar Covalent Bonds and Hydrogen Bonds (Fig 2.4, Fig 2.5, Fig 13.3)
Sometimes when a covalent bond forms between atoms of two different elements, the electrons are not shared equally. When this happens, a polar covalent bond results. example: H₂O.

Because of the polar nature of the covalent bonds in water, each molecule of water can form a hydrogen bond to as many as 4 other water molecules. Liquid water at 4^oC averages 3.6 H-bonds per water molecule. In ice, where solid water forms an open crystal-like structure, there are 4 H-bonds per water molecule.

Although each H-bond is a very weak association, the sheer quantity of H-bonds that are possible (a teaspoon of water contains 1.67 x 10²³ molecules of water) means that water shows a lot of cohesion (like sticking to like).   Water also shows adhesion (sticking to different molecules).

water resists temperature changes (a good temperature buffer)

The polar nature of water also means:
water is an excellent solvent for other polar molecules (like dissolves like)
water is an excellent solvent for salts/ions
water will hydrate large molecules that have polar groups (hydrophilic)

Molecules of Life

The four major classes of biological molecules:
 

polymers	monomers
carbohydrates (starch, cellulose)	sugars (glucose)
proteins	amino acids (20 to choose from)
lipids (fats or oils = triglycerides)	fatty acids (+ glycerol)
nucleic acids (DNA, RNA)	nucleotides (sugar, phosphate, N-base)

monomer vs. polymer
mer = unit
mono = one
poly = many
polymers are made many identical (starch) or similar (proteins) monomers

The monomers are joined by covalent bonds to make the polymers. Water is released as the covalent bonds form = condensation reaction (or dehydration synthesis).
(When the polymers are broken down - or digested - to release the monomers, water is added to break the covalent bond = hydrolysis reaction.)

all of the biological molecules contain C and H; most have O

Carbohydrates
monosaccharides:  hexoses (glucose, fructose), pentoses, trioses
disaccharides: sucrose
polysaccharides: starch, cellulose

Functions of carbohydrates:
1. Structural
        Cell wall
2. Storage of food (calories) in seeds, roots, stems, wood, bark, leaves
        Starch
        Sucrose
3. Transport of calories and carbon skeletons to make other molecules
        Sucrose

Proteins
contain N and some S (two of the 20 amino acids have S)
Polymers of amino acids
The bond between amino acids is called a peptide bond. Therefore, proteins are sometimes called polypeptides.
The 20 amino acids have the same basic format, differing only in what is known as the R group.

Functions of proteins
1. Structural
        Cell wall
        Cellular membranes
2. Storage
        Seeds, roots, stems: storage of calories and N
3. Enzymes
        catalysts: speed up chemical reactions but are not consumed or changed by the reactions
        As enzymes, proteins are responsible for all of the metabolic reactions and the synthesis of all of the other molecules found in organisms (carbohydrates, pigments, hormones, etc.)

Lipids
Functions of lipids
1. Storage
        triglycerides (triacylglycerides, TAGs): 
                for calorie storage, are usually found just in seeds. Exceptions: fruit of avocado, olive
2. Structural
        phospholipids in cell membranes
                     spontaneously form a bilayer in water: two hydrophilic surfaces with a hydrophobic interior; basis of membrane structure and function
        waxes:  long chain fatty acids + long chain alcohols
        cutin: in cuticle, which covers above ground plant parts
        suberin: in cell walls of the endodermis (roots, pine needles) and cork cells (bark)

Nucleic Acids 
DNA, RNA; important monomer = ATP

A single DNA molecule has:
a. many genes = information to make proteins (amino acid polymers)
b. genetic regulatory information = when to make a particular protein: development, response to environment; where to make a particular protein: seed, leaf

Overwhelmingly, the proteins made are enzymes. The actions of the enzymes (making pigments, making hormones, etc.) give an organism its physical attributes.

Secondary Metabolites

produced by a limited number of plants
generally not viewed as involved in essential metabolic and developmental processes 
historically, studied as "natural products"

As secondary metabolites are studied more extensively from a plant perspective rather than an economic botany perspective, we are finding that they serve the following functions for plants:
1. protective agents, such as antimicrobial agents and herbivory deterrents
2. attractants for animal pollination vectors or seed/fruit dispersers
3. allelopathy

The three most prominent types of molecules that are secondary metabolites:
phenolics
terpenes
alkaloids

Other Important Metabolites
organic acids
lignin
photosynthetic pigments

For illustrations to supplement those in your textbook, see:

http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCHEM1.html

http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCHEM2.html

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8 January 2011